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Coexpression cluster:C4469: Difference between revisions

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|tf_chipseq_enrich=REST#5978;3:9.65002871612802:0.00111263624711459:0.00770267910727831
|tf_chipseq_enrich=REST#5978;3:9.65002871612802:0.00111263624711459:0.00770267910727831
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}}
}}

Revision as of 16:45, 26 November 2012


Full id: C4469_Endothelial_lung_spleen_placenta_Hepatic_adipose_skeletal



Phase1 CAGE Peaks

Hg19::chr5:141337686..141337697,-p2@PCDH12
Hg19::chr5:141337703..141337712,-p4@PCDH12
Hg19::chr5:141337739..141337772,-p1@PCDH12


Enriched pathways on this co-expression cluster<b>Summary:</b><br>Canonical pathway gene sets were compiled from Reactome, Wikipathways and KEGG. For the major signaling pathways, the transcriptionally-regulated genes (downstream targets) were obtained from Netpath. Combined, the canonical pathways and downstream targets totaled 489 human gene sets. The corresponding M. musculus gene sets were inferred by homology using the HomoloGene database. Enrichment for each of the canonical 489 pathways and gene sets included in the co-expression cluster was assessed by the hypergeometric probability. The resulting P values were also then adjusted by the Benjamini-Hochberg method for multiple comparisons.<br><b>Analyst: </b>Emmanuel Dimont<br><br>link to source dataset<br>data


No results for this coexpression

Enriched Gene Ontology terms on this co-expression cluster<b>Summary:</b> Results for GOStat analysis on co-expressed clusters. Each cluster with promoters mapping to at least two different genes was analysed with GOStat (PMID: 14962934) with default parameter. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br>data


No GOStat results

Enriched sample ontology terms on this co-expression cluster<b>Summary:</b>To summarize promoter activities (expression profile of a TSS region) across ~1000 samples, we performed enrichment analysis based on FANTOM5 Sample Ontology (FF ontology). The question here is “in which type of samples the promoter is more active”. To answer this question, we compared expressions (TPMs) in the samples associated with a sample ontology term and the rest of the samples by using the Mann-Whitney rank sum test. To summarize ontologies enriched in this co-expression cluster, we ran the same analysis on an averaged expression profile of all promoters that make up. <b>Analyst:</b> Hideya Kawaji <br><br>links to source dataset<br><br>cell_data<br>uberon_data<br><br>


Uber Anatomy
Ontology termp-valuen
blood vessel endothelium8.79e-3118
endothelium8.79e-3118
cardiovascular system endothelium8.79e-3118
adult organism3.73e-27114
simple squamous epithelium3.55e-2422
squamous epithelium1.27e-2025
endothelial tube9.36e-199
arterial system endothelium9.36e-199
endothelium of artery9.36e-199
vessel2.20e-1868
splanchnic layer of lateral plate mesoderm1.21e-1583
vasculature7.22e-1578
vascular system7.22e-1578
circulatory system8.25e-15112
epithelial tube open at both ends3.57e-1359
blood vessel3.57e-1359
blood vasculature3.57e-1359
vascular cord3.57e-1359
anatomical cluster6.53e-13373
cardiovascular system1.90e-12109
anatomical conduit1.95e-12240
lymphoid system2.80e-1110
epithelial tube1.87e-10117
tube4.72e-09192
lymphatic vessel9.95e-098
lymph vasculature9.95e-098
lymphatic part of lymphoid system9.95e-098
microcirculatory vessel1.50e-073
endothelium of capillary1.50e-073
capillary1.50e-073
vein3.03e-079
venous blood vessel3.03e-079
venous system3.03e-079
compound organ3.35e-0768
multi-cellular organism5.94e-07656


Overrepresented TFBS (DNA) motifs on this co-expression cluster<b>Summary:</b>The values shown are the p-values for overrepresentation of the motif in this coexpression cluster. So a small p-value means a strong overrepresentation. <b>Analyst:</b> Michiel de Hoon <br><br>link to source data <br> Novel motifs <br>data <br><br> Jaspar motifs <br>data


Novel motifs



JASPAR motifs

Motifs-log10(p-value)

{{{tfbs_overrepresentation_jaspar}}}



ENCODE TF ChIP-seq peak enrichment analysis<b>Summary:</b> For each TF and each co-expression cluster, the number of promoters with ENCODE TF ChIP signal was compared with the rest of promoters from the robust set using Fisher's exact test. Clusters with significant ChIP enrichment (q <= 0.05) after Benjamini-Hochberg correction were retained. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br><br>data


(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
REST#597839.650028716128020.001112636247114590.00770267910727831



Relative expression of the co-expression cluster<b>Summary:</b>Co-expression clusters are compared against FANTOM5 samples to obtain relative expression. <br><b>Analyst:</b>NA<br><br>link to data source<br> data


This analysis result is provided for C0 - C305 clusters.